Helper function returning alignment for Grantham distance calculations

Helper function returning alignment for Grantham distance calculations

hlaAlignmentGrantham(gene, aa_sel = 2:182)

Arguments

gene

Character vector specifying HLA gene.

aa_sel

Numeric vector specifying amino acids that should be extracted.

Value

HLA alignment processed for grantham distance calculation. Processing includes extracting specific amino acids, masking indels, gaps and stop codons.